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SnpSift Split

Simply split (or join) VCF files. Allows to create one file per chromosome or one file every N lines.

A typical usage for this command is to:

  1. Split very large VCF files SnpSift split huge.vcf
  2. Perform some CPU intensive processing in parallel using several computers or cores
  3. Join the resulting VCF files SnpSift split -j huge.000.vcf huge.001.vcf huge.002.vcf ... > huge.out.vcf.

E.g.: Splitting a VCF having human variants:

java -jar SnpSift.jar split myHugeVcf.vcf.gz

Will create files myHugeVcf.1.vcf, myHugeVcf.2.vcf, ... , myHugeVcf.22.vcf, myHugeVcf.X.vcf, myHugeVcf.Y.vcf

You can also specify '-l' command line option to split the file every N lines.

E.g.: Split a VCF file every 10,000 lines:

java -jar SnpSift.jar split -l 10000 myHugeVcf.vcf.gz

Will create files myHugeVcf.001.vcf, myHugeVcf.002.vcf, ...


VCF header will be added to each file, so resulting files will be more than 10,000 lines.

You can use -j (join) command line option to join a set of VCF files.

java -jar SnpSift.jar split -j huge.000.vcf huge.001.vcf huge.002.vcf ...  > huge.out.vcf